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Coexpression cluster:C843: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!2.29e-29!79;UBERON:0007798!2.29e-29!79;UBERON:0003914!3.51e-27!118;UBERON:0004872!1.72e-26!84;UBERON:0000055!1.05e-25!69;UBERON:0005256!7.29e-25!143;UBERON:0001981!7.44e-24!60;UBERON:0007500!7.44e-24!60;UBERON:0004537!7.44e-24!60;UBERON:0006965!7.44e-24!60;UBERON:0000486!3.70e-23!82;UBERON:0000914!5.52e-23!83;UBERON:0002329!5.52e-23!83;UBERON:0003077!5.52e-23!83;UBERON:0003059!5.52e-23!83;UBERON:0007282!5.52e-23!83;UBERON:0009618!5.52e-23!83;UBERON:0007285!5.52e-23!83;UBERON:0002100!8.94e-23!216;UBERON:0004290!1.97e-21!70;UBERON:0000490!2.42e-21!138;UBERON:0004535!2.65e-20!110;UBERON:0001009!2.99e-20!113;UBERON:0001637!2.17e-19!42;UBERON:0003509!2.17e-19!42;UBERON:0004572!2.17e-19!42;UBERON:0001134!1.38e-18!61;UBERON:0002036!1.38e-18!61;UBERON:0003082!1.38e-18!61;UBERON:0000119!2.09e-18!312;UBERON:0002385!4.82e-18!63;UBERON:0001015!4.82e-18!63;UBERON:0000383!4.82e-18!63;UBERON:0000483!9.67e-18!309;UBERON:0000468!1.13e-17!659;UBERON:0003104!8.76e-17!238;UBERON:0009142!8.76e-17!238;UBERON:0000467!2.26e-15!625;UBERON:0000475!4.34e-15!365;UBERON:0000480!4.63e-15!626;UBERON:0000926!7.59e-15!448;UBERON:0004120!7.59e-15!448;UBERON:0006603!7.59e-15!448;UBERON:0004573!2.52e-14!33;UBERON:0004571!2.52e-14!33;UBERON:0000481!2.45e-13!347;UBERON:0000477!4.92e-11!286;UBERON:0002050!5.24e-11!605;UBERON:0005423!5.24e-11!605;UBERON:0000923!5.46e-11!604;UBERON:0005291!5.46e-11!604;UBERON:0006598!5.46e-11!604;UBERON:0002532!5.46e-11!604;UBERON:0001986!7.81e-11!18;UBERON:0004638!7.81e-11!18;UBERON:0004852!7.81e-11!18;UBERON:0000922!1.34e-10!612;UBERON:0000487!1.36e-10!22;UBERON:0006914!3.25e-10!25;UBERON:0004111!3.30e-10!241;UBERON:0003103!3.75e-09!69;UBERON:0000353!8.85e-09!17;UBERON:0004211!9.16e-09!16;UBERON:0001285!9.16e-09!16;UBERON:0007684!9.16e-09!16;UBERON:0003220!9.16e-09!16;UBERON:0004208!9.16e-09!16;UBERON:0006555!2.08e-08!17;UBERON:0005103!2.08e-08!17;UBERON:0000083!2.08e-08!17;UBERON:0009201!2.08e-08!17;UBERON:0004819!2.08e-08!17;UBERON:0006553!2.08e-08!17;UBERON:0003074!2.08e-08!17;UBERON:0003060!2.08e-08!17;UBERON:0000947!2.25e-08!21;UBERON:0010191!2.25e-08!21;UBERON:0000025!5.07e-08!194;UBERON:0004876!7.68e-08!20;UBERON:0003102!8.77e-08!95;UBERON:0000080!9.24e-08!18;UBERON:0002120!9.24e-08!18;UBERON:0004875!9.24e-08!18;UBERON:0005721!9.24e-08!18;UBERON:0005754!9.24e-08!18;UBERON:0007297!9.24e-08!18;UBERON:0001225!1.28e-07!13;UBERON:0008987!1.28e-07!13;UBERON:0009569!2.37e-07!113;UBERON:0006554!7.80e-07!44
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}}
}}

Revision as of 20:53, 8 August 2012


Full id: C843_Alveolar_Mesenchymal_Hepatic_Placental_Renal_Smooth_Fibroblast



Phase1 CAGE Peaks

Hg19::chr16:90015139..90015208,+p1@DEF8
Hg19::chr17:3571863..3571881,-p1@TAX1BP3
Hg19::chr18:12308232..12308252,+p1@TUBB6
Hg19::chr19:47354061..47354076,-p2@AP2S1
Hg19::chr1:113249721..113249731,-p3@RHOC
Hg19::chr1:113249734..113249762,-p1@RHOC
Hg19::chr1:113249948..113250035,-p4@RHOC
Hg19::chr2:242447692..242447726,-p4@STK25
Hg19::chr2:242447732..242447779,-p2@STK25
Hg19::chr5:176074455..176074519,+p1@TSPAN17


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0030128clathrin coat of endocytic vesicle0.0322402009543343
GO:0030669clathrin-coated endocytic vesicle membrane0.0322402009543343
GO:0030122AP-2 adaptor complex0.0322402009543343
GO:0030666endocytic vesicle membrane0.0322402009543343
GO:0003924GTPase activity0.0322402009543343
GO:0045334clathrin-coated endocytic vesicle0.0322402009543343
GO:0006901vesicle coating0.0322402009543343
GO:0048268clathrin cage assembly0.0322402009543343
GO:0006900membrane budding0.0322402009543343
GO:0005515protein binding0.0322402009543343
GO:0030132clathrin coat of coated pit0.0418403982307954
GO:0016050vesicle organization and biogenesis0.047192048562374
GO:0030178negative regulation of Wnt receptor signaling pathway0.048998473354561



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
mesodermal cell2.93e-37119
embryonic cell7.63e-37248
non-terminally differentiated cell2.43e-33180
somatic cell1.26e-22591
contractile cell3.74e-2259
animal cell5.28e-22679
eukaryotic cell5.28e-22679
muscle precursor cell3.64e-2057
myoblast3.64e-2057
multi-potent skeletal muscle stem cell3.64e-2057
muscle cell2.03e-1954
smooth muscle cell1.22e-1742
smooth muscle myoblast1.22e-1742
electrically responsive cell2.76e-1760
electrically active cell2.76e-1760
vascular associated smooth muscle cell3.38e-1532
lining cell4.48e-1557
barrier cell4.48e-1557
meso-epithelial cell4.93e-1544
epithelial cell1.25e-14254
endothelial cell5.95e-1435
fibroblast5.40e-1375
endothelial cell of vascular tree1.19e-1224
blood vessel endothelial cell7.81e-1118
embryonic blood vessel endothelial progenitor cell7.81e-1118
native cell2.08e-09722
epithelial cell of nephron9.16e-0916
squamous epithelial cell1.59e-0862
kidney cell1.02e-0718
kidney epithelial cell1.02e-0718
kidney cortical cell1.28e-0713
renal cortical epithelial cell1.28e-0713
Uber Anatomy
Ontology termp-valuen
vasculature2.29e-2979
vascular system2.29e-2979
epithelial tube3.51e-27118
splanchnic layer of lateral plate mesoderm1.72e-2684
vessel1.05e-2569
trunk mesenchyme7.29e-25143
blood vessel7.44e-2460
epithelial tube open at both ends7.44e-2460
blood vasculature7.44e-2460
vascular cord7.44e-2460
multilaminar epithelium3.70e-2382
somite5.52e-2383
paraxial mesoderm5.52e-2383
presomitic mesoderm5.52e-2383
presumptive segmental plate5.52e-2383
trunk paraxial mesoderm5.52e-2383
presumptive paraxial mesoderm5.52e-2383
trunk8.94e-23216
dermomyotome1.97e-2170
unilaminar epithelium2.42e-21138
cardiovascular system2.65e-20110
circulatory system2.99e-20113
artery2.17e-1942
arterial blood vessel2.17e-1942
arterial system2.17e-1942
skeletal muscle tissue1.38e-1861
striated muscle tissue1.38e-1861
myotome1.38e-1861
cell layer2.09e-18312
muscle tissue4.82e-1863
musculature4.82e-1863
musculature of body4.82e-1863
epithelium9.67e-18309
multi-cellular organism1.13e-17659
mesenchyme8.76e-17238
entire embryonic mesenchyme8.76e-17238
anatomical system2.26e-15625
organism subdivision4.34e-15365
anatomical group4.63e-15626
mesoderm7.59e-15448
mesoderm-derived structure7.59e-15448
presumptive mesoderm7.59e-15448
systemic artery2.52e-1433
systemic arterial system2.52e-1433
multi-tissue structure2.45e-13347
anatomical cluster4.92e-11286
embryonic structure5.24e-11605
developing anatomical structure5.24e-11605
germ layer5.46e-11604
embryonic tissue5.46e-11604
presumptive structure5.46e-11604
epiblast (generic)5.46e-11604
endothelium7.81e-1118
blood vessel endothelium7.81e-1118
cardiovascular system endothelium7.81e-1118
embryo1.34e-10612
simple squamous epithelium1.36e-1022
squamous epithelium3.25e-1025
anatomical conduit3.30e-10241
compound organ3.75e-0969
parenchyma8.85e-0917
nephron epithelium9.16e-0916
nephron9.16e-0916


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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